This actually always happened with Pd-ext as far as I remember. Each time I start Pd-ext, the Einblendeffekt (animation? can't find a translation) gets activated. This effect is what makes the windows "travel" when they're being minimized or maximized. You find it in
- right-click on the desktop
- 4th Tab [Darstellung], display??
- 1st checkbox, [use the next effects for menus and quickinfos]
[the menu names were translated by me from german, they might not be correct]